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A newly discovered virus has been found by a San Diego State University team to live inside more than half of all human gut cells sampled. Exploring genetic material found in intestinal samples, the international team uncovered the CrAssphage virus. They say the virus could influence the behaviour of some of the most common bacteria in our gut. Researchers say the virus has the genetic fingerprint of a bacteriophage - a type of virus known to infect bacteria. Phages may work to control the behaviour of bacteria they infect - some make it easier for bacteria to inhabit in their environments while others allow bacteria to become more potent. [Study lead Dr. Robert] Edwards said: "In some way phages are like wolves in the wild, surrounded by hares and deer. "They are critical components of our gut ecosystems, helping control the growth of bacterial populations and allowing a diversity of species." According to the team, CrAssphage infects one of the most common types of bacteria in our guts.
National Geographic gives some idea why a virus so common in our gut should have evaded discovery for so long, but at least CrAssphage finally has a Wikipedia page of its own.

I know! This virus serves a great and useful purpose: its eats that nasty and redundant CR character that Windowz and friends like to insert as part of their line endings. In other words, this gut-living virus eats crap. Bring it on!

The Nat Geo article states that crAss stands for the technique used to piece together fragments of the virus's genome: "They called it crAssphage after the cross-assembly method that revealed its existence."

A base pair is 2 bits of information. So it's actually around 24KB of information. And a reading frame is just a valid start point in the DNA. Codons are 3 base pairs, but only a couple of combinations start a reading frame.

FRY: This is a great, as long as you don't make me smell Uranus.... I'm sorry, Fry, but astronomers renamed Uranus in 2620 to end that stupid joke once and for all. FRY: Oh. What's it called now? PROFESSOR FARNSWORTH: Urectum.

Sometimes somebody else gives you a crass name, as a way of mocking you, such as Anal as an abbreviation for Analytical. And then you're stuck with it, love it or not. You yourself would have probably chosen a more respectable name, so with a name like this there may be a reason to look for tension, Abel-Kain or racism related social and psychological issues with the people that came up with the name. What a fun task for all these humanities college graduates analyzing the anthropological/psycho-sexual-freu

There's a bigger problem with the summary than that - timothy has misread the BBC article, which refers to 'half of all samples from the gut'. These aren't human cell samples, they're faecal samples. The phage presumably infects gut bacteria, not human cells. From the proteins that the phage encodes, the researchers predict the genus of bacteria the host belongs to (Bacteroides).

Yeah, not everything is Obama's fault. Lots of things are, but the EPA is a good thing. So is OSHA. Without them we have things like shown on http://www.filtersfast.com/art... [filtersfast.com] to which should be added Fukushima and West, TX fertilizer disasters (which is why urea is a safer nitrogen fertilizer than ammonium nitrate, but requires a carbon source, such as coal or oil or natural gas, to make. On the other hand ammonium nitrate makes a great explosive for makeshift bombs and makeshift ammo for self defense if s

Any virus is a form of life, in that it is negative entropy, in an entropy tending universe. Life seeks to create order, and maintain order, oftentimes in a fight, at an expense of another life form. A virus, because it cannot sustain itself on its own, has no functioning cell or nucleus, it is a parasite, a predator of other life. A predators function in an ecology is extremely complex, but there is one rule to any long term successful predator or parasite, is that you don't exterminate your food supply, y

I'm fuckin insane, dood. I'm the illest nigga on this block. Hold me back, hold me back, or I'll tell it like it is, in yo face, mutha fuckas. They are trying to turn me into some kind of terrorist, through some psychological warfare. Terrorist in the making. Fuck that. The only kind of terrorist I'll ever be is a verbal one, plug ya eeyas if u don't like it. I'll make y'all feel uncomfortable, and nobody is safe, I'll pick equally on everybody. And if you don't like it, you don't have to read my post, just

I'm the last author on the paper and it was discovered in my bioinformatics lab in the CS department [sdsu.edu] at SDSU [sdsu.edu]...

It was named after our analysis software, crAss (cross assembly) for comparing DNA sequences from different samples (called metagenomics [wikipedia.org]). Here is the crAss article [nih.gov] that was published in 2012. Everyone else had missed this virus that was in their DNA samples, most of which have been published (many in high profile journals like Science and Nature). However, it wasn't until we used crAss that we recognized the virus was abundant and everywhere. When we looked at the NCBI [nih.gov] database of nucleotide sequences the virus is there and scientists had seen it before in fragments but not been able to piece it together to a whole genome.

We only find the phage in poo samples (they usually call them fecal samples...) from people (oh, and very occasionally on the skin of people, but we suspect they don't have great hygiene). We haven't been able to find it anywhere else that we have looked, and so we don't know what its range is beyond the intestine.

This is one of those situations where the computational biology is really driving the question and the biologists. You often head that bioinformatics is just a support science for "real biology" - that's not true. In this case, based on the questions the bioinformatics group came up with, the biology was supporting the bioinformatics analysis. The biologists were able to determine that the assembly of DNA fragments was correct, and confirm, using PCR [wikipedia.org], that it is indeed a whole genome.

We (and others) are working on isolating the phage and designing experiments to test exactly what it does in our guts. That doesn't mean we can't speculate!

A couple of answers to comments:1. Everyone (including the scientists that write grants and papers) confuses gut and fecal samples (sometimes deliberately). To be clear, almost all the samples we have are feces because it is everyone has it, it is easy to get, and everyone seems to want to share it. To get samples other than feces you need surgery, and so the non-fecal samples tend to be associated with other issues that require surgical intervention (and thus are complicated).2. Noriko (Nori) Cassman is a graduate student (and so doesn't have tenure yet)3. We were not responsible for the wikipedia page (or the twitter account)4. phages are viruses that attack bacteria only. There is no evidence or suggestion that this virus does anything to human cells.

In one of the early versions of the paper we didn't have a name for it and just called it "the new virus". A (anonymous) reviewer said "The new virus would seem to need a name ("the new virus" is clumsy).", so we came up with crAssphage. It turns out there was an unexpected side benefit - there were essentially no Google results for crassphage until last week!

I'm the last author on the paper and it was discovered in my bioinformatics lab in the CS department at SDSU...

Quick question -- I see from your paper, do you have an idea what it looks structurally? A bunch of media sites have pictures but are using what is obviously stock art (mostly of T-even phages), but from your paper I see that it has no close phylogenetic relationship to known phages (and if your group had e-microscopy or crystallographic data, it would have been in the paper already).

Still, I figured someone skilled in virology might be able to identify some capsid sequences or something, and be able to ma

We don't have that capability yet. We have not isolated the virus, yet, (we're trying hard...) and so we don't have EMs of the particle which would tell us the T-number and other information, and our computational tools are not yet able to take a raw protein sequence, like that we can predict from the DNA sequence, and predict what the structure would look like. There are lots of groups working on that prediction step, and an annual competition (Critical Assessment of protein Structure Prediction) to see wh

Google has just recently started a "Google X" project to create a complete picture of what a healthy human being should be. [slashdot.org] Google should
be all over this if they really want a complete picture. Their commitment to studying the human genome could give afflicted people legitimate hope that their condition can be properly diagnosed. They may not find a cure for anything in X amount of years but at least they are on the right track.

The human genome is only a small part of what you are, the microbiome and virome (the microbial and viral components, respectively) have profound impacts on our health in ways that we really don't tet understand. However, this is an area where big data approaches that Google are good at will succeed. The only reason we found crAssphage is by comparing a lot of samples from different people. Imagine if we have genomes, microbiomes, and viromes from thousands of volunteers, together with health data about the

We have looked at quite a few animal samples, and it is not that common. There are a few mouse studies, but many of those now have "humanized" gut bacteria! They actually make the mouse look like the human!

We think it is mostly human associated, but it would sure be good to sequence some poo from chimps and apes to see if we can figure out where it is in our evolutionary tree. But that is not something we're going to do... hopefully others will.

Hit over 50% worldwide infection rate, then start buying the symptoms that kill and spread. Just make sure you've infected the islands before they cut off water and air travel (Greenland, Iceland, Madagascar, New Guinea and New Zealand have defeated me often enough).
Oh, and target the countries that are contributing the most to finding a cure.